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Nickel in PDB 6bi4: 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad.

Enzymatic activity of 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad.

All present enzymatic activity of 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad.:
4.2.1.46;

Protein crystallography data

The structure of 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad., PDB code: 6bi4 was solved by A.S.Halavaty, M.Kuhn, L.Shuvalova, G.Minasov, W.F.Anderson, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.95 / 2.91
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 165.557, 165.557, 292.121, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.4

Nickel Binding Sites:

The binding sites of Nickel atom in the 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad. (pdb code 6bi4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad., PDB code: 6bi4:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6bi4

Go back to Nickel Binding Sites List in 6bi4
Nickel binding site 1 out of 2 in the 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni401

b:1.0
occ:1.00
 OE1 C:GLU72 1.8 0.5 1.0
OE1 A:GLU72 2.2 0.8 1.0
NE2 A:HIS68 2.6 62.5 1.0
NE2 C:HIS68 2.6 67.8 1.0
OE2 A:GLU72 2.7 0.3 1.0
CD C:GLU72 2.7 0.9 1.0
CD A:GLU72 2.7 0.9 1.0
CD2 C:HIS68 2.9 59.4 1.0
OE2 C:GLU72 3.0 0.3 1.0
CD2 A:HIS68 3.2 60.2 1.0
CE1 A:HIS68 3.7 64.5 1.0
CE1 C:HIS68 3.9 71.8 1.0
CG C:GLU72 4.0 96.9 1.0
CG A:GLU72 4.2 98.5 1.0
CG C:HIS68 4.2 58.5 1.0
CB C:GLU72 4.3 81.0 1.0
CG A:HIS68 4.5 56.6 1.0
ND1 C:HIS68 4.6 71.5 1.0
CB A:GLU72 4.7 84.0 1.0
ND1 A:HIS68 4.7 63.5 1.0
O C:HIS68 4.9 50.8 1.0
CG2 C:VAL69 4.9 62.5 1.0

Nickel binding site 2 out of 2 in 6bi4

Go back to Nickel Binding Sites List in 6bi4
Nickel binding site 2 out of 2 in the 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni401

b:0.7
occ:1.00
 OE1 D:GLU72 2.0 95.8 1.0
OE1 B:GLU72 2.3 71.0 1.0
NE2 D:HIS68 2.4 61.7 1.0
NE2 B:HIS68 2.6 47.7 1.0
OE2 B:GLU72 2.8 98.5 1.0
CD2 D:HIS68 2.8 57.0 1.0
CD D:GLU72 2.8 99.8 1.0
CD B:GLU72 2.9 92.1 1.0
OE2 D:GLU72 3.1 0.3 1.0
CD2 B:HIS68 3.2 45.6 1.0
CE1 D:HIS68 3.7 72.6 1.0
CE1 B:HIS68 3.7 49.7 1.0
CG D:HIS68 4.1 57.7 1.0
CG D:GLU72 4.2 94.6 1.0
CG B:GLU72 4.3 79.3 1.0
CB D:GLU72 4.4 72.2 1.0
ND1 D:HIS68 4.5 74.2 1.0
CG B:HIS68 4.5 44.3 1.0
ND1 B:HIS68 4.7 48.3 1.0
CB B:GLU72 4.8 66.4 1.0
O D:HIS68 4.9 48.2 1.0
CG2 D:VAL69 4.9 47.2 1.0

Reference:

A.S.Halavaty, M.Kuhn, L.Shuvalova, G.Minasov, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6-Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad. To Be Published.
Page generated: Thu Oct 10 08:19:09 2024

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